A immunohistologic pilot study was completed which assessed interleukin-6 (IL-6), mast cell infiltrates, and serotonin (5-HT) levels on gastrointestinal tissue biopsies, with degrees of perceived abdominal pain in two groups, inflammatory and non-inflammatory pediatric gastrointestinal (GI) disorders. Methods: Clinical data and biopsy samples from pediatric patients with chronic abdominal pain, with and without inflammation, who underwent an outpatient endoscopic visit with biopsies were included in this study. Formalin-fixed paraffin-embedded GI biopsies were sectioned and immunohistochemistry performed for IL-6 and 5-HT;mast cells were identified with Giemsa staining. The association of histologic findings to self-reported abdominal pain and inflammation were evaluated statistically. Results: There was a significantly greater IL-6 immunoreactivity in biopsies with confirmed histologic inflammation compared to biopsies without inflammation (2(2)=10.9;p=.004). In comparison to the inflammatory group, the non-inflammatory group was significantly less likely (2(3)=10.12;p=.018) to respond to standard of care treatment as evidenced by higher pain reports(1.13.62 non-inflammatory vs. 1.94.69 inflammatory). Mast cells (p=.022) and 5-HT (p=.02) were significantly related to abdominal pain intensity scores. There was a negative correlation between abdominal pain intensity scores with mast cells (r= -.42) and 5-HT (r= -.52);whereas inflammatory phenotype (r=.55) was positively correlated. There was no significant differences between inflammatory and non-inflammatory groups for 5-HT (2(3)=4.08;p=.25). Conclusion: Mast cell number and 5-HT immunoreactivity correlate in GI biopsies from pediatric patients perceived abdominal pain intensity. Potential associations were demonstrated between self-reported abdominal pain intensity, the number of mast cell, and 5-HT levels, which may contribute to perceived abdominal pain by interacting with neuronal afferents in the gastrointestinal tract(submitted for publication). The aforementioned pilot study informed and provided justification for a prospective clinical natural history protocol. This Brain-Gut Natural History protocol(approved in January 2009) has to date enrolled 32 participants of which 28 have completed the protocol. The intestinal permeablity test solution was developed and tested. A pilot study was completed of serum IL-6 levels in healthy controls. The plan for the next fiscal year is to continue to enroll participants during the two year recruitment phase. Additional pilot testing and validation of the biomarkers will be undertaken, and the technology being developed will be refined. Further findings were published regarding symptom distress in other comorbid digestive diseases. One such study found that children have significant symptoms and physiologic liver changes related to hepatitis C virus. A significant relationship was found between hepatitis C genotype and clinical and socio-demographic indicators in this pediatric cohort (Henderson et al., 2009). In another cohort of patients, bio-behavioral predictors of hepatocellular carcinoma in hepatitis C virus patients with end-stage renal disease.It was found that Asian Americans are at three times the risk of developing hepatocelluar carcinoma. The co-morbidities of substance abuse and cirrhosis were also highly predictive of liver cancer (Henderson et al., 2009). The psychometric properties of a patient questionnaires for patients with liver disease co-morbidities was tested and validated(Henderson et al., in press).